Notes: Abbott began his career as Sternberg's assistant in the Biological Laboratory at Hopkins in 1884, where he aided in the extensive studies on chemical disinfectants. In 1885, he was Welch's assistant at Hopkins, and began employing Koch's methods that Welch brought back from Germany. Abbott had as his first student, W.D. Booker, who conducted studies of infant diarrhea. Abbott and Welch were the first in America to confirm the organism responsible for diphtheria, and under Welch's direction, Abbott studied the relationship between water supplies and epidemics. The mortality rate from typhoid fever was shockingly high in Philadelphia, averaging between 50 and 75 annual deaths per 100,000. Abbott described in 1886, Vibrio schuylkiliensis, one of the number of spiral organisms that were often confused with V. cholera. In 1886, Welch sent Abbott to study with von Pettenkofer and with Koch in Germany.

When the Laboratory of Hygiene at Penn opened in 1892, Abbott was the first assistant to J. S. Billings, and provided bacteriological instruction to medical students and other qualified students.

Abbott's Principles, published originally in 1892, survived more than forty years, appearing in edition after edition. McFarland mentions: "In the beginning it may have fulfilled the requirements of the newly instituted brief courses in bacteriology that were being offered...but as the years and decades passed and the subject grew, it lost value with each edition, yet for some mysterious reason the new editions continued to appear. It is to be deplored that Abbott did not improve his book so as to make and keep it abreast of the times as long as he lived.”

While heading the Laboratory of Hygiene of U Penn, he was a candidate for the dir. of the Lab. of Hygiene for the Bur. of Health in Phil. But, the health dept. wanted him full time. Only when Bolton resigned after a year, did Abbott take over, all the while still keeping his work at Penn. Abbott expanded the work of the lab from diphtheria exams to the Widal test.

As director of hygienic lab, Abbott changed the focus from that of Billings, emphasizing research in bacteriology rather than general hygiene. Along with Jordan and Conn, Abbott was primarily responsible for the organization of the SAB. He presented a paper at the second meeting in 1900, on "Branching Forms of the Diphtheria Bacillus," which was not included on the printed program, and was discussed by Hill, Chester, Park, Gorham and Harris.

In the 1902 paper on the acid resisting group, Abbott and Gildersleeve conclude that 1) the majority of the related bacteria may be "distinguished from true tubercle bacilli by their inability to resist decolorization by a 30% solution of nitric acid," 2) some of the acid resisting bacteria "are capable of causing in rabbits and guinea pigs nodular lesions suggestive of tuberculosis", but not usually in the lungs, nor disseminated, and 3) don't produce the usual lesions in hogs and calves, 4) that "though occasionally present in dairy products, they are to be regarded as of no significance, etiologically speaking, but may be considered as accidental contaminations from the surroundings, and not as evidence of disease in the animals," and 5) that the designation 'bacillus' is "a misnomer; they are more correctly classified as actinomyces."

At the 1903 meeting of the AAPB, Abbott presented a paper on the proteolytic enzymes in immunologic reactions.

Abbott re appears on the SAB program in 1914, as part of a joint session with section K of the AAAS, on "Ventilation." Abbott discussed "Ventilation in Its Relation to Air Borne Diseases," in which he strongly denied the likelihood of frequent transmission via air, and claimed that it was "of infinitely less importance than transmission by animate and inanimate carriers that have been in intimate contact with the patient."